This directory contains the Oct. 2010 (WS220/ce10) assembly of the
C. elegans genome (ce10, Washington University School of Medicine
GSC and Sanger Institute WS220), as well as repeat annotations and
GenBank sequences.
This assembly was produced by the Genome Sequencing Center at the
Washington University in St. Louis (WUSTL) School of Medicine and
the Sanger Institute. For more information on the
C. elegans genome, see the WUSTL project website at
http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+elegans.
and WormBase information:
http://wiki.wormbase.org/index.php/Caenorhabditis_elegans
This UCSC sequence data was downloaded from:
ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_elegans/
Files included in this directory:
ce10.2bit - contains the complete C. elegans/ce10 genome sequence
in the 2bit file format. Repeats from RepeatMasker and Tandem Repeats
Finder (with period of 12 or less) are shown in lower case; non-repeating
sequence is shown in upper case. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
chromAgp.tar.gz - Description of how the assembly was generated from
fragments, unpacking to one file per chromosome.
chromFa.tar.gz - The assembly sequence in one file per chromosome.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
RepeatMasker was run with the -s (sensitive) setting.
RepeatMasker version:
June 30 2010 (open-3-2-9) version of RepeatMasker
CC RELEASE 20090604
chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED 5+
format (one file per chromosome).
est.fa.gz - C. elegans ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - C. elegans mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts of RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it might be slightly out of sync with
the RefSeq data which is updated daily for most assemblies.
upstream2000.fa.gz - Same as upstream1000, but 2000 bases.
upstream5000.fa.gz - Same as upstream1000, but 5000 bases.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
ce10.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
ce10.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
ce10.gc5Base.wig.gz - wiggle database table for the GC Percent track
- this is an older standard alternative to the current
- bigWig format of the track, sometimes usefull for analysis
ce10.gc5Base.wib - binary data to correspond with the gc5Base.wig file
see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html
and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
for a discussion of how to use the wig.gz and .wib files for
interaction with the GC percent data values
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If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/ce10/bigZips. To download multiple files, use
the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/ce10/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/ce10/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce10/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce10/bigZips/chromFa.tar.gz'
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
------------------------------------------------------------------------
The C. elegans sequence is made freely available to the community by the
Genome Sequencing Center at the WUSTL School of Medicine. Please see the
WUSTL data use policy at http://genome.wustl.edu/data.cgi for data use
restrictions and citation information.
------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
ce10.2bit 2011-05-23 13:23 25M
ce10.chrom.sizes 2011-05-23 11:38 99
ce10.fa.gz 2020-01-23 02:20 30M
ce10.gc5Base.wib 2019-01-17 14:44 19M
ce10.gc5Base.wig.gz 2019-01-17 14:44 360K
ce10.gc5Base.wigVarStep.gz 2011-05-23 11:39 51M
chromAgp.tar.gz 2011-06-09 16:24 55K
chromFa.tar.gz 2011-06-09 16:24 30M
chromFaMasked.tar.gz 2011-06-09 16:25 26M
chromOut.tar.gz 2011-06-09 16:24 2.7M
chromTrf.tar.gz 2011-06-09 16:25 190K
est.fa.gz 2019-10-16 21:35 72M
est.fa.gz.md5 2019-10-16 21:35 44
genes/ 2020-02-05 13:46 -
md5sum.txt 2019-01-17 15:52 623
mrna.fa.gz 2019-10-16 21:19 1.7M
mrna.fa.gz.md5 2019-10-16 21:19 45
refMrna.fa.gz 2019-10-16 21:35 17M
refMrna.fa.gz.md5 2019-10-16 21:35 48
upstream1000.fa.gz 2019-10-16 21:35 3.7M
upstream1000.fa.gz.md5 2019-10-16 21:35 53
upstream2000.fa.gz 2019-10-16 21:36 6.9M
upstream2000.fa.gz.md5 2019-10-16 21:36 53
upstream5000.fa.gz 2019-10-16 21:36 16M
upstream5000.fa.gz.md5 2019-10-16 21:36 53
xenoMrna.fa.gz 2019-10-16 21:30 6.8G
xenoMrna.fa.gz.md5 2019-10-16 21:30 49
xenoRefMrna.fa.gz 2019-10-16 21:35 314M
xenoRefMrna.fa.gz.md5 2019-10-16 21:35 52